Table of Contents

Remove water and ions from trajs

Open a and add the following lines:

trajin rec.all.mdcrd
strip :WAT,Na+,Cl-
trajout rec.mdnw.mdcrd

Now enter ptraj <

But if you need some waters around your ligand or QMMM region? No problem! Forget 'strip' and add these lines to your

solvent byres :WAT
closestwater 20 :464 first (WAT around residue 464 until 20 A of distance will be preserved)